Mercurial > repos > mvdbeek > r_goseq_1_22_0

comparison goseq.xml @ 17:1b03f6232900 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
author mvdbeek
date Fri, 26 Feb 2016 08:49:59 -0500
parents fe71b97cc1a5
children 5fb82111ec62
comparison
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16:8ce951313688 17:1b03f6232900
1 <tool id="goseq" name="goseq gene ontology analyser" version="0.1.1"> 1 <tool id="goseq" name="goseq gene ontology analyser" version="0.1.4">
2 <description /> 2 <description />
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.2.1">R</requirement> 4 <requirement type="package" version="3.2.1">R</requirement>
5 <requirement type="package" version="1.22.0">goseq</requirement> 5 <requirement type="package" version="1.22.0">goseq</requirement>
6 </requirements> 6 </requirements>
7 <command interpreter="Rscript"> 7 <command interpreter="Rscript">
8 goseq.r --dge_file "$dge_file" 8 goseq.r --dge_file "$dge_file"
9 --p_adj_column "$p_adj_column" 9 --p_adj_column "$p_adj_column"
10 --cutoff "$p_adj_cutoff" 10 --cutoff "$p_adj_cutoff"
11 #if $source.use_length_file == "yes":
12 --length_file "$length_file"
13 #end if
11 --genome "$genome" 14 --genome "$genome"
12 --gene_id "$gene_id" 15 --gene_id "$gene_id"
13 --wallenius_tab "$wallenius_tab" 16 --wallenius_tab "$wallenius_tab"
14 --sampling_tab "$sampling_tab" 17 --sampling_tab "$sampling_tab"
15 --nobias_tab "$nobias_tab" 18 --nobias_tab "$nobias_tab"
17 --sample_vs_wallenius_plot "$sample_vs_wallenius_plot" 20 --sample_vs_wallenius_plot "$sample_vs_wallenius_plot"
18 --repcnt "$repcnt" 21 --repcnt "$repcnt"
19 </command> 22 </command>
20 <inputs> 23 <inputs>
21 <param help="deseq2/edger/limma differential gene expression list" label="DGE list" name="dge_file" type="data" format="tabular" /> 24 <param help="deseq2/edger/limma differential gene expression list" label="DGE list" name="dge_file" type="data" format="tabular" />
22 <param help="Select the column that contains the multiple-testing corrected p-value" label="p adjust column" name="p_adj_column" type="data_column" data_ref="dge_file"/> 25 <param help="Select the column that contains the multiple-testing corrected p-value" label="p adjust column" name="p_adj_column" type="data_column" numeric="true" data_ref="dge_file"/>
23 <param help="Typically 0.05 after multiple testing correction" max="1" label="Minimum p adjust value to consider gene differentially expressed" name="p_adj_cutoff" type="float" value="0.05" /> 26 <param help="Typically 0.05 after multiple testing correction" max="1" label="Minimum p adjust value to consider genes as differentially expressed" name="p_adj_cutoff" type="float" value="0.05" />
24 <param help="Needed to retrive gene length for length correction" label="Select the genome source" name="genome" size="3" type="select"> 27 <conditional name="source">
25 <options from_file="genomes.loc"> 28 <param help="This is needed if the gene length is not available in goseq. e.g. hg38 and mm10." label="Use gene length file?" name="use_length_file" type="select">
26 <column name="value" index="0"/> 29 <option value="no">no</option>
27 <column name="name" index="1"/> 30 <option value="yes">yes</option>
28 </options> 31 </param>
32 <when value="yes">
33 <param label="Gene length file" name="length_file" type="data" format="tabular" required="false" />
34 </when>
35 <when value="no">
36 </when>
37 </conditional>
38 <param help="Needed to retrieve gene length for length correction" label="Select the genome source" name="genome" size="3" type="select">
39 <options from_data_table="go_genomes"></options>
29 </param> 40 </param>
30 <param help="Needed for GO analysis" label="Select gene identifier" name="gene_id" type="select"> 41 <param help="Needed for GO analysis" label="Select gene identifier" name="gene_id" type="select">
31 <options from_file="gene_ids.loc"> 42 <options from_data_table="go_gene_ids"></options>
32 <column name="value" index="0"/>
33 <column name="name" index="1"/>
34 </options>
35 </param> 43 </param>
36 <param help="Do this many random samplings. Larger values take a long time" label="Number of random sampling" name="repcnt" size="3" type="integer" min="100" max="10000" value="1000" /> 44 <param help="Draw this many random control gene sets. Set to 0 to not do sampling. Larger values take a long time" label="sampling depth" name="repcnt" size="3" type="integer" min="0" max="10000" value="0" />
37 </inputs> 45 </inputs>
38 <outputs> 46 <outputs>
47 <data format="pdf" label="length bias plot" name="length_bias_plot" />
48 <data format="pdf" label="Plot P-value from sampling against wallenius distribution" name="sample_vs_wallenius_plot">
49 <filter>repcnt != 0</filter>
50 </data>
39 <data format="tabular" label="Ranked category list - wallenius" name="wallenius_tab" /> 51 <data format="tabular" label="Ranked category list - wallenius" name="wallenius_tab" />
40 <data format="tabular" label="Ranked category list - sampling" name="sampling_tab" /> 52 <data format="tabular" label="Ranked category list - sampling" name="sampling_tab">
53 <filter>repcnt != 0</filter>
54 </data>
41 <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" /> 55 <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" />
42 <data format="pdf" label="length bias plot" name="length_bias_plot" />
43 <data format="pdf" label="Plot P-value from sampling against wallenius distribution" name="sample_vs_wallenius_plot" />
44 </outputs> 56 </outputs>
45 <tests> 57 <tests>
46 <test> 58 <test>
47 59 <param name="dge_file" value="dge_list.tab" ftype="tabular"/>
60 <param name="use_length_file" value="no" />
61 <param name="p_adj_column" value="2" />
62 <param name="genome" value="hg19" />
63 <param name="gene_id" value="ensGene" />
64 <output name="wallenius_tab" file="wall.tab" compare="contains"/>/>
48 </test> 65 </test>
49 </tests> 66 </tests>
50 <help> 67 <help>
51 68
52 **What it does** 69 **What it does**
56 Options map closely to the excellent manual_ 73 Options map closely to the excellent manual_
57 74
58 .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf 75 .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf
59 76
60 77
61 </help> 78 </help>
62 <citations> 79 <citations>
63 <citation type="doi">10.1186/gb-2010-11-2-r14</citation> 80 <citation type="doi">10.1186/gb-2010-11-2-r14</citation>
64 </citations> 81 </citations>
65 </tool> 82 </tool>